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MRNA decay in E. coli

ABSTRACT: Half-lives of known and predicted E. coli mRNAs at single-gene resolution by using two-color fluorescent DNA microarrays. Groups of assays that are related as part of a time series. Keywords: time_series_design

ORGANISM(S): Escherichia coli

PROVIDER: GSE3267 | GEO | 2005/09/09

SECONDARY ACCESSION(S): PRJNA104809

REPOSITORIES: GEO

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mRNA decay in E. coli

Project description:Half-lives of known and predicted E. coli mRNAs at single-gene resolution by using two-color fluorescent DNA microarrays. Groups of assays that are related as part of a time series. User Defined

2005-09-09 | E-GEOD-3267 | biostudies-arrayexpress

Transcription profiling analysis of mRNA decay in E.coli

Project description:Half-lives of known and predicted E. coli mRNAs at single-gene resolution by using two-color fluorescent DNA microarrays.

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Global analysis of mRNA decay and abundance in Escherichia coli

Project description:Abstract: Much of the information available about factors that affect mRNA decay in Escherichia coli, and by inference in other bacteria, has been gleaned from study of less than 25 of the approximately 4,300 predicted E. coli messages. To investigate these factors more broadly, we examined the half-lives and steady-state abundance of known and predicted E. coli mRNAs at single-gene resolution by using two-color fluorescent DNA microarrays. An rRNA-based strategy for normalization of microarray data was developed to permit quantitation of mRNA decay after transcriptional arrest by rifampicin. We found that globally, mRNA half-lives were similar in nutrient-rich media and defined media in which the generation time was approximately tripled. A wide range of stabilities was observed for individual mRNAs of E. coli, although approximately 80% of all mRNAs had half-lives between 3 and 8 min. Genes having biologically related metabolic functions were commonly observed to have similar stabilities. Whereas the half-lives of a limited number of mRNAs correlated positively with their abundance, we found that overall, increased mRNA stability is not predictive of increased abundance. Neither the density of putative sites of cleavage by RNase E, which is believed to initiate mRNA decay in E. coli, nor the free energy of folding of 5' or 3' untranslated region sequences was predictive of mRNA half-life. Our results identify previously unsuspected features of mRNA decay at a global level and also indicate that generalizations about decay derived from the study of individual gene transcripts may have limited applicability. This SuperSeries is composed of the SubSeries listed below.

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RNA Abundance in E. coli

Project description:Steady-state abundance of known and predicted E. coli mRNAs at single-gene resolution by using two-color fluorescent DNA microarrays. Set of arrays organized by shared biological context, such as organism, tumors types, processes, etc. Keywords: Logical Set

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RNA Abundance in E. coli

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mRNA decay data set

Project description:Groups of assays that are related as part of a time series. Keywords: time_series_design

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Global SLAM-Seq for accurate mRNA decay determination and identification of NMD targets

Project description:Gene expression analysis requires accurate measurements of global RNA degradation rates, earlier problematic with methods disruptive to cell physiology. Recently, metabolic RNA labeling emerged as an efficient and minimally invasive technique applied in mammalian cells. Here, we have adapted SH-Linked Alkylation for the Metabolic Sequencing of RNA (SLAM-Seq) for a global mRNA stability study in yeast using 4-thiouracil pulse-chase labeling. We assign high-confidence half-life estimates for 67.5 % of expressed ORFs, and measure a median half-life of 9.4 min. For mRNAs where half-life estimates exist in the literature, their ranking order was in good agreement with previous data, indicating that SLAM-Seq efficiently classifies stable and unstable transcripts. We then leveraged our yeast protocol to identify targets of the Nonsense-mediated decay (NMD) pathway by measuring the change in RNA half-lives; instead of steady-state RNA level changes. With SLAM-Seq, we assign 580 transcripts as putative NMD targets, based on their measured half-lives in wild-type and upf3Δ mutants. We find 225 novel targets, and observe a strong agreement with previous reports of NMD targets, 61.2 % of our candidates being identified in previous studies.This indicates that SLAM-Seq is a simpler and more economic method for global quantification of mRNA half-lives. Our adaptation for yeast yielded global quantitative measures of the NMD effect on transcript half-lives, high correlation with RNA half-lives measured previously with more technically challenging protocols, and identification of novel NMD regulated transcripts that escaped prior detection.

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Examination of mRNA decay rate in mouse embryonic fibroblasts

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